thackl / minidot

Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2

minidot

Quickly produce pretty dotplots from minimap mappings using R/ggplot2.

Dependencies

• R packages: ggplot2, stringr, scales, argparse
• curl, gzip (for samples only)

Install

git clone https://github.com/thackl/minidot.git

Samples

make sample-prochlorococcus
make sample-arabidopsis

Make sample commands will download required data, set up minimap (if not already in $PATH) and run minidot.

Prochlorococcus ecotypes

# actual minidot command invoked by make sample-prochlorococcus after setting up the data
minidot -s -o prochlorococcus.pdf MED4.da SB.fa NATLA2.fa LG.fa MIT9313.fa

Quickly compare genome organization among multiple bacterial genomes (finished and draft).

A. thaliana vs A. lyrata - compare two related eukaryotes

# actual minidot command invoked by make sample-arabidopsis after setting up the data
minidot -o arabidopsis.pdf A.lyrata.fa A.thaliana.fa

Compare two related eukaryotic genomes. Larger genomes are automatically run in fast mode, which is less sensitive and looks only for larger stretches of similarity (>500bp).

For A.t. vs A.l., mapping & plotting takes about 1.5 minutes (desktop PC, 3 threads, 8GB RAM). That’s probably faster than downloading the genomes in the first place…

Contact

Any kind of feedback is highly appreciated. Feel free to either report issues directly via github or shoot me an email.